*Target (protein/gene name): 1-deoxy-D-xylulose-5-phosphate reductoisomerase *NCBI Gene # or RefSeq#: HP0216 *Protein ID (NP or XP #) or Wolbachia#:NP_207014.1 *Organism (including strain): Helicobacter pylori Etiologic Risk Group (see link below): *Background/Disease Information (sort of like the Intro to your Mini Research Write up): Essentiality of this protein:
1-Deoxy-D-xylulose 5-phosphate reductoisomerase (DXR) is a key enzyme of the pathway that catalyzes the rearrangement and nicotinamide adenine dinucleotide phosphate (NADPH)-dependent reduction of 1-deoxy-D-xylulose 5-phosphate (DXP) to MEP. The unique properties of DXR make it a remarkable and rational target for drug design. First, it is a vital enzyme for synthesis of isoprenoids in algae, plants, several eubacteria including the pathogenic bacteria like Bacillus anthracis, Helicobacter pylori, Yersinia pestis, Mycobacterium tuberculosis and the malarial parasite, Plasmodium falciparum. Second, there are no functional equivalents to DXR in humans, making it an attractive target for therapeutic intervention. Third, DXR appears to be a valid target and the results from fosmidomycin (1), the only available DXR inhibitor under clinical trials, suggests synergistic effects with the lincosamide antibiotics, lincomycin and clindamycin.
reference:
Targeting the methyl erythritol phosphate (MEP) pathway for novel antimalarial, antibacterial and herbicidal drug discovery: inhibition of 1-deoxy-D-xylulose-5-phosphate reductoisomerase (DXR) enzyme.
Nidhi Singh, Gweneal Chevé, Mitchell A. Avery, Christopher R. McCurdy
Curr Pharm Des. 2007; 13(11): 1161–1177.
Complex of proteins?: Druggable Target:
*EC#: Link to BRENDA EC# page: --Show screenshot of BRENDA enzyme mechanism schematic Enzyme Assay information (spectrophotometric, coupled assay ?, reagents): -- link to Sigma (or other company) page for assay or assay reagents (substrates) -- link (or citation) to paper that contains assay information -- List cost and quantity of substrate reagents and supplier Structure Available (PDB or Homology model)
-- PDB # or closest PDB entry if using homology model: 3A14
-- For Homology Model option:
---- Show pairwise alignment of your BLASTP search in NCBI against the PDB
---- Query Coverage:
---- Max % Identities: 34%
---- % Positives: 55%
---- Chain used for homology: B
Current Inhibitors:
fosmidomycin
Expression Information (has it been expressed in bacterial cells): Purification Method: Image of protein (PyMol with features delineated and shown separately): *Amino Acid Sequence (paste as text only - not as screenshot or as 'code'):
>fid|32015|locus|HP0216| 1-deoxy-D-xylulose 5-phosphate reductoisomerase [Helicobacter pylori 26695] MVVLGSTGSIGKNALKIAKKFGIEIEALSCGKNIALINEQIQVFKPKKVAILDPSDLNDL EPLGAEVFVGLEGIDAMIEECTSNLVLNAIVGVAGLKASFKSLQRNKKLALANKESLVSA GHLLDISQITPIDSEHFGLWALLQNKTLKPKSLIISASGGAFRDTPLEFIPIQNAQNALK HPNWSMGSKITIDSASMVNKLFEILETYWLFGASLKIDALIERSSIVHALVEFEDNSIIA HLASADMQLPISYAIDPKLASLSASIPLDLYALSAIKFEPISMERYTLWCYKDLLLENP KLGVVLNASNEVAMEKFLNKEIAFGGLIQTISQALESYDKMPFKLSSLEEVLELDKEVRE RFKNVAGV
*length of your protein in Amino Acids
368
Molecular Weight of your protein in kiloDaltons using the Expasy ProtParam website
40270.9
Molar Extinction coefficient of your protein at 280 nm wavelength:
30940
TMpred graph Image (http://www.ch.embnet.org/software/TMPRED_form.html). Input your amino acid sequence to it. *CDS Gene Sequence (paste as text only):
>gi|15644634:224692-225798 Helicobacter pylori 26695 chromosome, complete genome ATGGTTGTTTTAGGAAGCACCGGCTCTATTGGGAAAAACGCCCTAAAAATCGCAAAAAAATTTGGCATAG AAATAGAGGCCTTAAGCTGTGGGAAAAATATCGCTTTAATCAATGAACAAATCCAAGTTTTCAAACCCAA GAAAGTGGCGATTTTAGATCCTAGCGATTTGAATGATTTAGAGCCTTTGGGTGCGGAAGTGTTTGTGGGG TTAGAGGGCATTGATGCGATGATAGAAGAGTGCACCTCAAATTTAGTCCTTAACGCCATTGTGGGCGTGG CAGGATTGAAAGCGAGCTTTAAAAGCTTACAAAGGAATAAAAAACTGGCCCTAGCGAATAAAGAAAGCTT AGTGAGCGCGGGGCATTTATTAGACATTTCACAAATCACGCCCATTGATAGCGAGCATTTTGGTTTGTGG GCGTTGTTGCAAAACAAGACTTTAAAGCCTAAATCCTTAATCATTAGCGCGAGTGGGGGGGCTTTCAGGG ACACGCCTTTAGAATTTATTCCTATTCAAAACGCGCAAAATGCGCTCAAGCACCCTAATTGGAGCATGGG ATCTAAAATCACCATTGATTCAGCGAGCATGGTCAATAAGCTTTTTGAAATCCTAGAAACTTATTGGCTT TTTGGCGCGTCTTTAAAGATTGATGCGCTGATTGAAAGGAGTTCTATCGTGCATGCTTTGGTGGAGTTTG AAGACAACTCTATCATCGCGCATTTAGCGAGCGCAGATATGCAATTACCCATAAGCTATGCGATCGATCC GAAGTTGGCCTCTTTGAGCGCGTCTATCAAGCCCTTAGATCTATACGCTTTAAGCGCGATTAAATTTGAA CCCATTAGCATGGAGCGCTACACTTTGTGGTGTTATAAAGACTTACTGCTAGAAAACCCTAAGCTTGGCG TGGTGCTGAATGCGAGCAATGAAGTGGCGATGGAGAAGTTTTTAAACAAAGAGATCGCTTTTGGTGGCCT TATCCAAACCATTTCTCAAGCCTTAGAATCATACGATAAAATGCCTTTCAAGCTCTCTAGTTTAGAAGAA GTGCTGGAATTAGACAAAGAAGTTAGGGAGCGTTTTAAAAATGTAGCGGGAGTGTAG
*GC% Content for gene: *CDS Gene Sequence (codon optimized) - copy from output of Primer Design Protocol (paste as text only): *GC% Content for gene (codon optimized):
Do Not Need this info for Spring (but still copy these lines to your Target page for now) Primer design results for pNIC-Bsa4 cloning (list seqeunces of all of your ~40 nt long primers): (link to DNA Works output text file - that should be saved in your Google Docs folder after you did the primer design protocol)
-- Ask a mentor, Dr. B, or a fellow researcher -how to link a GDocs file if you are not sure how to.
Primer design results for 'tail' primers (this is just 2 sequences):
*NCBI Gene # or RefSeq#: HP0216
*Protein ID (NP or XP #) or Wolbachia#:NP_207014.1
*Organism (including strain): Helicobacter pylori
Etiologic Risk Group (see link below):
*Background/Disease Information (sort of like the Intro to your Mini Research Write up):
Essentiality of this protein:
1-Deoxy-D-xylulose 5-phosphate reductoisomerase (DXR) is a key enzyme of the pathway that catalyzes the rearrangement and nicotinamide adenine dinucleotide phosphate (NADPH)-dependent reduction of 1-deoxy-D-xylulose 5-phosphate (DXP) to MEP. The unique properties of DXR make it a remarkable and rational target for drug design. First, it is a vital enzyme for synthesis of isoprenoids in algae, plants, several eubacteria including the pathogenic bacteria like Bacillus anthracis, Helicobacter pylori, Yersinia pestis, Mycobacterium tuberculosis and the malarial parasite, Plasmodium falciparum. Second, there are no functional equivalents to DXR in humans, making it an attractive target for therapeutic intervention. Third, DXR appears to be a valid target and the results from fosmidomycin (1), the only available DXR inhibitor under clinical trials, suggests synergistic effects with the lincosamide antibiotics, lincomycin and clindamycin.
reference:
Targeting the methyl erythritol phosphate (MEP) pathway for novel antimalarial, antibacterial and herbicidal drug discovery: inhibition of 1-deoxy-D-xylulose-5-phosphate reductoisomerase (DXR) enzyme.
Nidhi Singh, Gweneal Chevé, Mitchell A. Avery, Christopher R. McCurdy
Curr Pharm Des. 2007; 13(11): 1161–1177.
Complex of proteins?:
Druggable Target:
*EC#:
Link to BRENDA EC# page:
-- Show screenshot of BRENDA enzyme mechanism schematic
Enzyme Assay information (spectrophotometric, coupled assay ?, reagents):
-- link to Sigma (or other company) page for assay or assay reagents (substrates)
-- link (or citation) to paper that contains assay information
-- List cost and quantity of substrate reagents and supplier
Structure Available (PDB or Homology model)
-- PDB # or closest PDB entry if using homology model: 3A14
-- For Homology Model option:
---- Show pairwise alignment of your BLASTP search in NCBI against the PDB
---- Query Coverage:
---- Max % Identities: 34%
---- % Positives: 55%
---- Chain used for homology: B
Current Inhibitors:
fosmidomycin
Expression Information (has it been expressed in bacterial cells):
Purification Method:
Image of protein (PyMol with features delineated and shown separately):
*Amino Acid Sequence (paste as text only - not as screenshot or as 'code'):
>fid|32015|locus|HP0216| 1-deoxy-D-xylulose 5-phosphate reductoisomerase [Helicobacter pylori 26695] MVVLGSTGSIGKNALKIAKKFGIEIEALSCGKNIALINEQIQVFKPKKVAILDPSDLNDL EPLGAEVFVGLEGIDAMIEECTSNLVLNAIVGVAGLKASFKSLQRNKKLALANKESLVSA GHLLDISQITPIDSEHFGLWALLQNKTLKPKSLIISASGGAFRDTPLEFIPIQNAQNALK HPNWSMGSKITIDSASMVNKLFEILETYWLFGASLKIDALIERSSIVHALVEFEDNSIIA HLASADMQLPISYAIDPKLASLSASIPLDLYALSAIKFEPISMERYTLWCYKDLLLENP KLGVVLNASNEVAMEKFLNKEIAFGGLIQTISQALESYDKMPFKLSSLEEVLELDKEVRE RFKNVAGV
*length of your protein in Amino Acids
368
Molecular Weight of your protein in kiloDaltons using the Expasy ProtParam website
40270.9
Molar Extinction coefficient of your protein at 280 nm wavelength:
30940
TMpred graph Image (http://www.ch.embnet.org/software/TMPRED_form.html). Input your amino acid sequence to it.
*CDS Gene Sequence (paste as text only):
>gi|15644634:224692-225798 Helicobacter pylori 26695 chromosome, complete genome ATGGTTGTTTTAGGAAGCACCGGCTCTATTGGGAAAAACGCCCTAAAAATCGCAAAAAAATTTGGCATAG AAATAGAGGCCTTAAGCTGTGGGAAAAATATCGCTTTAATCAATGAACAAATCCAAGTTTTCAAACCCAA GAAAGTGGCGATTTTAGATCCTAGCGATTTGAATGATTTAGAGCCTTTGGGTGCGGAAGTGTTTGTGGGG TTAGAGGGCATTGATGCGATGATAGAAGAGTGCACCTCAAATTTAGTCCTTAACGCCATTGTGGGCGTGG CAGGATTGAAAGCGAGCTTTAAAAGCTTACAAAGGAATAAAAAACTGGCCCTAGCGAATAAAGAAAGCTT AGTGAGCGCGGGGCATTTATTAGACATTTCACAAATCACGCCCATTGATAGCGAGCATTTTGGTTTGTGG GCGTTGTTGCAAAACAAGACTTTAAAGCCTAAATCCTTAATCATTAGCGCGAGTGGGGGGGCTTTCAGGG ACACGCCTTTAGAATTTATTCCTATTCAAAACGCGCAAAATGCGCTCAAGCACCCTAATTGGAGCATGGG ATCTAAAATCACCATTGATTCAGCGAGCATGGTCAATAAGCTTTTTGAAATCCTAGAAACTTATTGGCTT TTTGGCGCGTCTTTAAAGATTGATGCGCTGATTGAAAGGAGTTCTATCGTGCATGCTTTGGTGGAGTTTG AAGACAACTCTATCATCGCGCATTTAGCGAGCGCAGATATGCAATTACCCATAAGCTATGCGATCGATCC GAAGTTGGCCTCTTTGAGCGCGTCTATCAAGCCCTTAGATCTATACGCTTTAAGCGCGATTAAATTTGAA CCCATTAGCATGGAGCGCTACACTTTGTGGTGTTATAAAGACTTACTGCTAGAAAACCCTAAGCTTGGCG TGGTGCTGAATGCGAGCAATGAAGTGGCGATGGAGAAGTTTTTAAACAAAGAGATCGCTTTTGGTGGCCT TATCCAAACCATTTCTCAAGCCTTAGAATCATACGATAAAATGCCTTTCAAGCTCTCTAGTTTAGAAGAA GTGCTGGAATTAGACAAAGAAGTTAGGGAGCGTTTTAAAAATGTAGCGGGAGTGTAG
*GC% Content for gene:
*CDS Gene Sequence (codon optimized) - copy from output of Primer Design Protocol (paste as text only):
*GC% Content for gene (codon optimized):
Do Not Need this info for Spring (but still copy these lines to your Target page for now)
Primer design results for pNIC-Bsa4 cloning (list seqeunces of all of your ~40 nt long primers):
(link to DNA Works output text file - that should be saved in your Google Docs folder after you did the primer design protocol)
-- Ask a mentor, Dr. B, or a fellow researcher -how to link a GDocs file if you are not sure how to.
Primer design results for 'tail' primers (this is just 2 sequences):